6QQ1

Crystal structure of as isolated Y323F mutant of haem-Cu containing nitrite reductase from Ralstonia pickettii


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52840.1M HEPES (pH7.5), 20% PEG 3350, 0.2 M Sodium citrate
Crystal Properties
Matthews coefficientSolvent content
2.7355

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 128.291α = 90
b = 128.291β = 90
c = 86.177γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6Mmirrors2018-04-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97624DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.6165.15950.1130.12780.0550.9979.35.25877019.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.611.6462.51.140.560.5521.45.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONTHROUGHOUT1.7565.150094271698.940.13780.136360.16333RANDOM20.204
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-0.04-0.02-0.040.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.155
r_dihedral_angle_4_deg20.129
r_dihedral_angle_3_deg13.293
r_dihedral_angle_1_deg7.079
r_long_range_B_refined6.028
r_long_range_B_other5.514
r_scangle_other3.924
r_scbond_it2.589
r_scbond_other2.589
r_mcangle_it2.188
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.155
r_dihedral_angle_4_deg20.129
r_dihedral_angle_3_deg13.293
r_dihedral_angle_1_deg7.079
r_long_range_B_refined6.028
r_long_range_B_other5.514
r_scangle_other3.924
r_scbond_it2.589
r_scbond_other2.589
r_mcangle_it2.188
r_mcangle_other2.187
r_angle_refined_deg1.668
r_mcbond_it1.579
r_mcbond_other1.574
r_angle_other_deg1.453
r_chiral_restr0.08
r_bond_refined_d0.012
r_gen_planes_refined0.011
r_gen_planes_other0.006
r_bond_other_d0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3429
Nucleic Acid Atoms
Solvent Atoms520
Heterogen Atoms51

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
REFMACphasing